Matches in SemOpenAlex for { <https://semopenalex.org/work/W3173711206> ?p ?o ?g. }
Showing items 1 to 89 of
89
with 100 items per page.
- W3173711206 abstract "Abstract Background Metagenomic sequencing has led to the identification and assembly of many new bacterial genome sequences. These bacteria often contain plasmids: usually small, circular double-stranded DNA molecules that may transfer across bacterial species and confer antibiotic resistance. These plasmids are generally less studied and understood than their bacterial hosts. Part of the reason for this is insufficient computational tools enabling the analysis of plasmids in metagenomic samples. Results We developed SCAPP (Sequence Contents-Aware Plasmid Peeler)—an algorithm and tool to assemble plasmid sequences from metagenomic sequencing. SCAPP builds on some key ideas from the Recycler algorithm while improving plasmid assemblies by integrating biological knowledge about plasmids. We compared the performance of SCAPP to Recycler and metaplasmidSPAdes on simulated metagenomes, real human gut microbiome samples, and a human gut plasmidome dataset that we generated. We also created plasmidome and metagenome data from the same cow rumen sample and used the parallel sequencing data to create a novel assessment procedure. Overall, SCAPP outperformed Recycler and metaplasmidSPAdes across this wide range of datasets. Conclusions SCAPP is an easy to use Python package that enables the assembly of full plasmid sequences from metagenomic samples. It outperformed existing metagenomic plasmid assemblers in most cases and assembled novel and clinically relevant plasmids in samples we generated such as a human gut plasmidome. SCAPP is open-source software available from: https://github.com/Shamir-Lab/SCAPP ." @default.
- W3173711206 created "2021-07-05" @default.
- W3173711206 creator A5008335823 @default.
- W3173711206 creator A5018675044 @default.
- W3173711206 creator A5037199232 @default.
- W3173711206 creator A5038806020 @default.
- W3173711206 creator A5046895298 @default.
- W3173711206 creator A5085526613 @default.
- W3173711206 creator A5088912364 @default.
- W3173711206 date "2021-06-25" @default.
- W3173711206 modified "2023-10-18" @default.
- W3173711206 title "SCAPP: an algorithm for improved plasmid assembly in metagenomes" @default.
- W3173711206 cites W2048673910 @default.
- W3173711206 cites W2057411492 @default.
- W3173711206 cites W2089180338 @default.
- W3173711206 cites W2108234281 @default.
- W3173711206 cites W2119902463 @default.
- W3173711206 cites W2143325926 @default.
- W3173711206 cites W2782623083 @default.
- W3173711206 cites W2909601828 @default.
- W3173711206 cites W2942757983 @default.
- W3173711206 cites W2950530458 @default.
- W3173711206 cites W3014345701 @default.
- W3173711206 cites W3015282831 @default.
- W3173711206 doi "https://doi.org/10.1186/s40168-021-01068-z" @default.
- W3173711206 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/8228940" @default.
- W3173711206 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/34172093" @default.
- W3173711206 hasPublicationYear "2021" @default.
- W3173711206 type Work @default.
- W3173711206 sameAs 3173711206 @default.
- W3173711206 citedByCount "23" @default.
- W3173711206 countsByYear W31737112062020 @default.
- W3173711206 countsByYear W31737112062021 @default.
- W3173711206 countsByYear W31737112062022 @default.
- W3173711206 countsByYear W31737112062023 @default.
- W3173711206 crossrefType "journal-article" @default.
- W3173711206 hasAuthorship W3173711206A5008335823 @default.
- W3173711206 hasAuthorship W3173711206A5018675044 @default.
- W3173711206 hasAuthorship W3173711206A5037199232 @default.
- W3173711206 hasAuthorship W3173711206A5038806020 @default.
- W3173711206 hasAuthorship W3173711206A5046895298 @default.
- W3173711206 hasAuthorship W3173711206A5085526613 @default.
- W3173711206 hasAuthorship W3173711206A5088912364 @default.
- W3173711206 hasBestOaLocation W31737112061 @default.
- W3173711206 hasConcept C104317684 @default.
- W3173711206 hasConcept C141231307 @default.
- W3173711206 hasConcept C143121216 @default.
- W3173711206 hasConcept C15151743 @default.
- W3173711206 hasConcept C22744801 @default.
- W3173711206 hasConcept C51679486 @default.
- W3173711206 hasConcept C54355233 @default.
- W3173711206 hasConcept C552990157 @default.
- W3173711206 hasConcept C70721500 @default.
- W3173711206 hasConcept C86803240 @default.
- W3173711206 hasConceptScore W3173711206C104317684 @default.
- W3173711206 hasConceptScore W3173711206C141231307 @default.
- W3173711206 hasConceptScore W3173711206C143121216 @default.
- W3173711206 hasConceptScore W3173711206C15151743 @default.
- W3173711206 hasConceptScore W3173711206C22744801 @default.
- W3173711206 hasConceptScore W3173711206C51679486 @default.
- W3173711206 hasConceptScore W3173711206C54355233 @default.
- W3173711206 hasConceptScore W3173711206C552990157 @default.
- W3173711206 hasConceptScore W3173711206C70721500 @default.
- W3173711206 hasConceptScore W3173711206C86803240 @default.
- W3173711206 hasFunder F4320320950 @default.
- W3173711206 hasFunder F4320321821 @default.
- W3173711206 hasFunder F4320322252 @default.
- W3173711206 hasFunder F4320338335 @default.
- W3173711206 hasIssue "1" @default.
- W3173711206 hasLocation W31737112061 @default.
- W3173711206 hasLocation W31737112062 @default.
- W3173711206 hasLocation W31737112063 @default.
- W3173711206 hasOpenAccess W3173711206 @default.
- W3173711206 hasPrimaryLocation W31737112061 @default.
- W3173711206 hasRelatedWork W2293713895 @default.
- W3173711206 hasRelatedWork W2320874112 @default.
- W3173711206 hasRelatedWork W3043668926 @default.
- W3173711206 hasRelatedWork W3103414575 @default.
- W3173711206 hasRelatedWork W3111832393 @default.
- W3173711206 hasRelatedWork W3114049237 @default.
- W3173711206 hasRelatedWork W3141171859 @default.
- W3173711206 hasRelatedWork W3182597671 @default.
- W3173711206 hasRelatedWork W3203797096 @default.
- W3173711206 hasRelatedWork W4248693975 @default.
- W3173711206 hasVolume "9" @default.
- W3173711206 isParatext "false" @default.
- W3173711206 isRetracted "false" @default.
- W3173711206 magId "3173711206" @default.
- W3173711206 workType "article" @default.